TB-Profiler result

Run: ERR4827767
Summary

Run ID: ERR4827767

Sample name:

Date: 2024-04-15T07:01:01.020822

Number of reads: 3799875

Percentage reads mapped: 99.69

Median coverage: 118.0

Strain: lineage4.8

Spoligotype:

Drug-resistance: Other

Download CSV Download TXT Download JSON
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 1.0
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
ethambutol
pyrazinamide
streptomycin rpsL p.Lys43Arg Assoc w R
gid p.Arg206* Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence Comment
rpsL 781687 p.Lys43Arg missense_variant 0.31 streptomycin Assoc w R
gid 4407587 p.Arg206* stop_gained 0.6 streptomycin Assoc w R
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13569 c.-11C>A upstream_gene_variant 0.25 isoniazid Uncertain significance
Rv0010c 13626 c.-68T>C upstream_gene_variant 0.62 isoniazid Uncertain significance
mshA 576108 p.Ala254Gly missense_variant 0.32 ethionamide
isoniazid
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 0.99 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0 capreomycin Not assoc w R
linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
PPE35 2168149 p.Pro822Ser missense_variant 1.0 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv2680 2995848 c.-257G>A upstream_gene_variant 1.0 capreomycin
Rv2681 2997073 p.Leu112Arg missense_variant 0.14 capreomycin
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0 ethionamide Uncertain significance
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
ubiA 4269864 c.-31C>T upstream_gene_variant 0.92 ethambutol Uncertain significance
whiB6 4338596 c.-76_-75delAGinsCGA upstream_gene_variant 0.42 capreomycin
amikacin
kanamycin
whiB6 4338596 c.-75delG upstream_gene_variant 0.58 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338596 c.-76_-75delAGinsCGA upstream_gene_variant 0.42 capreomycin
amikacin
kanamycin
whiB6 4338596 c.-75delG upstream_gene_variant 0.58 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R